Alignment and same length

[picas...@gmail.com]

Dear Oligotyping community,

I'm not sure to understant the Alignment part of that page :

http://merenlab.org/2012/05/11/oligotyping-pipeline-explained/

First, I have PE reads that I trimmed then I merged, which result to unequal length. I get that we need equal length but I not sure when to trim:

1) Before the alignment or after the alignment ?
2) For the alignment, I use PyNast and gg_97_otus_6oct2010_aligned.fasta. SO when should I use : o-trim-uninformative-columns-from-alignment ?
before the trimming step (to get equal length reads) or after ?

[A. Murat Eren]

Hi,

If you did the trimming before merging partially overlapping PE Illumina reads, it still is the "Case 3" described here:

http://merenlab.org/2014/09/14/oligotyping-and-alignment/

Best,

--

A. Murat Eren (meren)
http://merenlab.org :: gpg

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[picas...@gmail.com]

So we do this before the alignment ?

[picas...@gmail.com]

SO I used that script :

o-pad-with-gaps

and perform the alignment but I got a weird error:

align_seqs.py -i myseq.fasta -t gg_13_8_otus/rep_set_aligned/97_otus.fasta -o out
Traceback (most recent call last):
  File "/home/user/qiime/bin/align_seqs.py", line 5, in <module>
    pkg_resources.run_script('qiime==1.9.1', 'align_seqs.py')
  File "/software/lib/python2.7/site-packages/pkg_resources.py", line 483, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/software/lib/python2.7/site-packages/pkg_resources.py", line 1341, in run_script
    execfile(script_filename, namespace, namespace)
  File "/Home/user/qiime/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg/EGG-INFO/scripts/align_seqs.py", line 211, in <module>
    main()
  File "/Home/user/qiime/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg/EGG-INFO/scripts/align_seqs.py", line 194, in main
    log_path=log_path, failure_path=failure_path)
  File "/home/user/qiime/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg/qiime/align_seqs.py", line 266, in __call__
    temp_dir=get_qiime_temp_dir())
  File "/home/user/.local/lib/python2.7/site-packages/pynast/util.py", line 812, in pynast_seqs
    for seq, status in pynast_iterator:
  File "/home/user/.local/lib/python2.7/site-packages/pynast/util.py", line 661, in ipynast_seqs
    raise ValueError, "Candidate sequence contains gaps. This is not supported."
ValueError: Candidate sequence contains gaps. This is not supported.


On Sunday, June 26, 2016 at 6:10:38 PM UTC+2, A. Murat Eren wrote: